The site of Christ's weeping was unmarked until the Crusader era. It was during this time that people began commemorating the site. Eventually a small chapel was built there. After the fall of Jerusalem in 1187, the church fell into ruin. In the early sixteenth century a mosque or madrasah existed at the site, presumably built by the Turks, from the remains of the earlier church, although the exact use is disputed. This place was known as el Mansouriyeh (The Triumphant) and also el Khelweh (The Hermitage).

View through the window of the church

The Franciscans were unable to obtain the ruins, so, in 1891 they purchased a small plot of land nearby and built a small chapel there. In 1913 a small private home was built in front of the Franciscan chapel by one Miss Mellon. This home eventually passed to the Sisters of St. Joseph, who eventually sold it to a Portuguese woman.

In 1940, the Benedictine Sisters sold part of the property to the Franciscans. The old boundary wall was moved at this time to make the division. In 1953 the Franciscans began construction of another wall. While digging the foundations, workers unearthed ancient tombs. Excavations began at the site, led by Fr. Bellarmino Bagatti, OFM.

A late Bronze Age tomb from the Canaanite period, as well as a necropolis used from 136 BC to 300 AD were discovered. The necropolis spanned two separate periods, characterized by differing tomb styles. The earlier Second Temple era tombs were of the Kokhim style, while the Byzantine era section was composed of tombs with arcosolium from the 3rd and 4th centuries AD. A Byzantine monastery from the 5th century was also discovered. Mosaics from this monastery still remain at the site.